There is nothing natural about giving birth in a wooden or metal box, and some does take a while to figure out that's what they are supposed to do . If the doe is grabbing mouthfuls of hay and pulling it out of the box and moving it to another corner, I'd move the box to that corner. If she starts working on yet another corner, I might stuff the entire cage with hay, in hopes of having enough material there to keep the kits warm enough to survive until I can find them and move them to the box. With most of my does, once a litter is in the box, they get the idea and subsequent litters are delivered in the box as expected.